Its just a workflow problem. You have to to any translations (moving,scaling etc) first on the original model that has the texture UVs on.
Then what I do is duplicate the tool divide up the triangulated model as much as your computer can handle and press "polypaint from texture".
Then I duplicate the original again, and either dynamesh or Zremesh the model. I'll UV that either in Maya or with UV master.
Then divide up the model if you need more resolution and project the details and polypaint from your high res model that has the polypaint texture onto the newly UV'd geometry.
Then you can transfer that to a bitmap and export it out if you want.
but for this process to work the models need to be in exactly the same position.